User:Eric Martz

Professor Emeritus, University of Massachusetts, Amherst MA USA

Personal website: martz.molviz.org My page on my Department's website.

Proteopedia Pages to Which I've Contributed
Unless otherwise indicated, these are pages that I created, and for which I provided the initial content. Below, -> or <- mean that one page redirects to another page.

Molecules: Topic Pages

 * I started a stub for Antibody. Article later written by User:David Canner and others.
 * Avian Influenza Neuraminidase, Tamiflu and Relenza
 * Flagella, bacterial <- Flagellum, Flagellar structure
 * Flagellar filament of bacteria
 * Flagellar hook of bacteria
 * Gramicidin Channel in Lipid Bilayer
 * Influenza hemagglutinin: I started a stub; article later written by User:Savannah Anderson and others.
 * Lac repressor
 * Major Histocompatibility Complex Class I
 * Mechanosensitive channels: opening and closing included MORPHS
 * Membrane proteins
 * Metal-Ligand Polyhedra
 * Nitrotyrosine
 * Proton Channels, which includes an animated morph.
 * Recoverin, a calcium-activated myristoyl switch
 * Structure of E. coli DnaC helicase loader (about a homology model)
 * SV40 Capsid Simplified
 * User:Eric Martz/Nucleosomes (a protected page for lectures), which was copied into Nucleosomes so others can improve it.

Molecules: PDB Code-Titled Pages

 * 1hgf Influenza hemagglutinin
 * 2ic8 (green links in overview)
 * 2rd0 Phosphatidylinositol kinase oncogene: I authored scenes similar to many of the figures from the publication.

Topic Pages: Lists of Other Pages

 * About Macromolecular Structure
 * High school teachers' resources <- K-12 teachers' resources, Secondary school teachers' resources
 * Research Groups and Institutes
 * Student Projects
 * Teaching Scenes, Tutorials, and Educators' Pages <- Molecule of the Month, MotM, Motm
 * See also Topic pages -> Proteopedia: Topic Pages

Topic Pages - Education
(Some of these pages are linked redundantly under other headings on this page.)


 * Adoptions in University Classes
 * High school teachers' resources <- K-12 teachers' resources, Secondary school teachers' resources
 * Molecular Workbench
 * Student Projects
 * Teaching Scenes, Tutorials, and Educators' Pages <- Molecule of the Month, MotM, Motm
 * Teaching Strategies Using Proteopedia
 * Technology-Enhanced Science Activities for STEMEd 6 Mar 2010

Topic Pages - Molecular Playground

 * Molecular Playground/Authoring
 * Molecular Playground/Procedures
 * CBI Molecules
 * 


 * Molecular Playground/HIV Protease Inhibitor
 * Molecular Playground/Relenza
 * Molecular Playground/Tamiflu

A-E

 * About Macromolecular Structure
 * Amino Acids
 * Asymmetric Unit UNIT CELL SCENE NOT WORKING
 * Atomic coordinate file <- PDB file, PDB file format
 * Biological Unit <- Quaternary structure
 * CASP
 * Cation-pi interactions was written largely by Wayne Decatur
 * Conservation, Evolutionary <- Evolutionary Conservation
 * ConSurfDB vs. ConSurf
 * CPK
 * Crystal contacts
 * DRuMS
 * Eric Martz's Favorites
 * Electron density maps
 * Epitopes
 * Evolutionary conservation: see Conservation
 * Extremophiles

F-M

 * Fadel A. Samatey Group also in Japanese
 * Free R
 * Hetero atoms
 * Highest impact structures of all time.
 * History of Macromolecular Visualization
 * Homology modeling
 * Homology modeling servers
 * Hydrogen bonds
 * Hydrogen in macromolecular models
 * Improving published models
 * Influenza
 * Intrinsically Disordered Protein authored largely by User:Tzviya Zeev-Ben-Mordehai
 * Ligand
 * Membrane proteins
 * Morphs of conformational changes of macromolecules

N-R

 * NMR Ensembles of Models <- NMR
 * Nobel Prizes for 3D Molecular Structure
 * PDB identification code <- PDB code, PDB codes, pdb code, pdb codes
 * Peptide (page created by Eran Hodis)
 * Personal favorites
 * Protein Data Bank <- PDB
 * Pyrrolysine
 * Ribosomal_A_Site_Binding_Paromomycin:_A_Morph
 * Quality assessment for molecular models
 * Remarkable Structures
 * R value
 * Resolution

S-Z

 * Salt bridges
 * Selenocysteine
 * Sites, Functional
 * Standard Residues and Non-Standard Residues
 * Structural alignment tools
 * Structural genomics
 * Structures_Gallery_Generator
 * Teaching Strategies Using Proteopedia
 * Temperature value <- B value, Disorder
 * Temperature value vs. resolution
 * Temperature color schemes
 * Theoretical models <- Theory, Theoretical model
 * X-ray crystallography <- X-ray diffraction

Topic Pages: People/Biographies

 * Richards, Frederic M.

Software

 * Molecular modeling and visualization software


 * Chime
 * FirstGlance in Jmol
 * Java
 * Jmol
 * Jmol/Application
 * Jmol/Visualizing large molecules
 * Kinemages, Mage and KiNG
 * Molecular Workbench
 * Protein Explorer
 * PyMOL
 * RasMol
 * Swiss-PDBViewer = DeepView

EMail List

 * Proteopedia:Email list

Help

 * Help:Color Keys
 * Help:Copying FirstGlance Scenes into Proteopedia
 * Help:Editing
 * Help:How to Insert a ConSurf Result Into a Proteopedia Green Link
 * Help:Language Translation
 * Help:Plain text editors
 * Help:Protected Pages
 * Help:Quiz
 * Help:Sandboxes
 * Help:Snapshots

Proteopedia

 * Mugs and T-Shirts: I created these products and set up the non-profit store at cafepress.com/molviz4.
 * News (disambiguation)
 * Proteopedia:About
 * Proteopedia:Languages
 * Proteopedia:Namespaces
 * Proteopedia:News
 * Proteopedia:Policy
 * Proteopedia:Problems
 * Proteopedia:Scrapbook
 * Proteopedia:Subdirectories
 * Proteopedia:Supplementary materials
 * Proteopedia:Topic Pages
 * Proteopedia:What's New <- What's New?, What's New, what's new, What's New in Proteopedia?
 * Proteopedia:Wishlist

Proteopedia Pages Using Jmol Color Key Legends

 * Gramicidin Channel in Lipid Bilayer
 * Metal-Ligand Polyhedra

Mediawiki

 * Special:Prefixindex/Mediawiki:
 * Special:Prefixindex/Mediawiki:Sat-tooltip

Templates

 * Template:Article_under_development
 * Template:ColorKey_N2CRainbow
 * Example of use: NMR_Ensembles_of_Models
 * Template:ColorKey_ConSurf
 * The Templates used on the DRuMS and Help:Color Keys pages. All begin "Template:ColorKey".
 * Template:Protected page banner
 * Example of use: User:Karl Oberholser/Ramachandran Plots
 * Template:Button Toggle Animation used at Lac repressor.


 * Template:Murthy_fraud
 * Template:Possible_fraud

(To find all templates contributed by a user, at the user's page, click User contributions (at left), then set the namespace to Templates.)

Pages by Others That I Especially Like
This is not a complete list -- it is a just a few that I want to be able to find easily in case I forget.


 * Ozonolysis

Workshops

 * One-day courses in molecular visualization and structural bioinformatics for researchers and educators.

Principal Author or Architect of (Elsewhere):

 * FirstGlance in Jmol, a general-purpose molecular visualization tool which has been adopted by Nature (see the 3D View links), the ConSurf Server, and other journals and structural bioinformatics servers. Available 2005-present.
 * Visualization for the the ConSurf Server developed by Nir Ben-Tal, Fabian Glaser, Elana Erez and others, which colors amino acids by evolutionary conservation, completely automatically. Available 2002-present.
 * Top Five 3D Molecular Visualization Technologies for the Rest Of Us. Page available 2007-present.
 * MolviZ.Org with tutorials in Jmol and molecular visualization resources for educators and students. Included is a DNA Structure Tutorial started in 1996, and now (in collaboration with Angel Herráez) available in 5 languages.
 * World Index of Molecular Visualization Resources. Available 2000-present.
 * Atlas of Macromolecules. Available 2002-present.
 * With Jaime Prilusky, the PDB Lite search interface for students and beginners to find published macromolecular models. Available 1998-2010 (decommisioned).
 * An incomplete History of Macromolecular Visualization which includes a list of the earliest macromolecules solved by X-ray crystallography. Available 1997-present.
 * molvis-list, founded in 1995 as the RasMol List. Maintained largely by Tim Driscoll/molvisions.com since 2004.

And in an earlier era


 * Protein Explorer 1998-present.
 * The RasMol Classic Site (formerly the RasMol Home Page) founded 1996. (The current RasMol Home Page is at RasMol.Org by Herbert Bernstein, available since 1999.)

Help

 * &lt;span style="font-size:150%"&gt;Samatey Group&lt;/span&gt;


 * Caption
 * [[Image:wiki.png|frame|Wikipedia Encyclopedia]]
 * Help:Editing
 * Images: Basic Markup  /    Full Image Syntax
 * Tables
 * Proteopedia:Cookbook
 * Rectangular Jmol
 * Image Maps
 * Theoretical Model Template
 * Floating Quote Box
 * Links in Applet Caption
 * Flash .swf
 * Template:Button_Toggle_Animation

PDB Examples

 * Sites (after 2nd remediation): 1uu1 (AC1); 1fws (AC1-6); 1sid (AC1-9, BC1-9, all "binding sites"); 1pop (AC1-AC9, BC1-BC9, CC1-CC6 all "binding sites" + CAT "CAT"); 1zzz (CAT "Active Site");

Files Uploaded

 * Files Uploaded by Eric Martz

Sandboxes Reserved for Teaching

 * Created by Eric: 1-161
 * Template:Sandbox Reserved Eric Martz 1-40 May-July 2011 Osaka Univ
 * Formerly Apr-Jun 2010 Osaka Univ
 * Template:Sandbox Reserved Eric Martz 2 41-60 Jan-Mar 2011 UMass
 * Formerly 41-100 Feb-Mar 2010 Israel and extra 151-161
 * Template:Sandbox Reserved Eric Martz 3 101-150 May-Jul 2010 UMass
 * Template:Sandbox Reserved Eric Martz 4

Sandboxes for Collaborations

 * Sandbox Eric Martz (not protected) DeShais Collaboration
 * Sandbox2 Eric Martz (not protected) ConSurfDB Collaboration
 * Sandbox3 Eric Martz (not protected) (deleted; was Samatey)
 * Sandbox4 Eric Martz (not protected) (available)
 * Sandbox 5 Eric Martz (not protected) Heme Morph (Prilusky)
 * Sandbox6 Eric Martz (not protected) PVLSI Scully Schwartz homol mod
 * Sandbox7 Eric Martz (not protected) (available)

Sandboxes: Protected

 * User:Eric Martz/Sandbox scrolling division test
 * User:Eric Martz/Sandbox 0 Knots in Proteins - see Methods in Sandbox 11
 * User:Eric Martz/Sandbox 2 FGiJ state script -> Proteopedia
 * User:Eric Martz/Sandbox 3 ConSurf mockup, also SandboxC
 * User:Eric Martz/Sandbox 4 Quiz testing
 * User:Eric Martz/Sandbox 5 News item mockup for *OLD* main page
 * User:Eric Martz/Sandbox 6 H274Y Tamiflu resistance mutation in N1
 * User:Eric Martz/Sandbox 7 PyMOL translator notes
 * User:Eric Martz/Sandbox 8 Water
 * User:Eric Martz/Sandbox 9 Tunnel
 * User:Eric Martz/Sandbox 10 hbonds
 * User:Eric Martz/Sandbox 11 knot methods
 * User:Eric Martz/Sandbox 12 links that perform searches
 * User:Eric Martz/Sandbox 13 Sequence Alignment Tools
 * User:Eric Martz/Sandbox 14 (available)


 * User:Eric Martz/liveConnect Test hyperlink to javascript applet.script(...): HTML not interpreted

Workbenches

 * User:Eric Martz/Workbench/Workbench01
 * User:Eric Martz/Workbench/Samatey Group
 * User:Fadel A. Samatey/Workbench/Samatey Group

Protected Topic Pages

 * User:Eric Martz/Remarkable Structures
 * User:Eric Martz/Nucleosomes (cf. Nucleosomes)


 * User:Eric Martz/Molecular Playground/Tamiflu
 * User:Eric Martz/Molecular Playground/HIVDrug
 * User:Eric Martz/Molecular Playground/Authoring

All Protected Pages

 * Special:Prefixindex/User:Eric_Martz
 * Search for User:Eric Martz in User Namespace

Other Quicklinks

 * Special:Wantedpages

Personal To Do List
-Email other educators, see google/wave. -Brewer's educational game project: structure-function-drug design as part of the challenges? -Draft email to pdb-l about either metal-ligand polyhedra or oleg's paper on "suppl mats" -See Comments -Enlarged HIV script -Knots